Got it!
Hi Hailiang,
Yes, you can run phenix.autobuild with your data file, sequence file, model (if any), maps_only=True and ncs_output_mask_file=my_mask_file.map and ncs_file=my_ncs.ncs_spec and it should write out a ccp4-style my_mask_file.map file showing the ncs asymmetric unit (in addition to generating map coefficients for a density-modified map).
The my_mask_file.map will be in AutoBuild_run_1_/TEMP0/
I used these commands just now to test it out (takes about 10 minutes; you can do the same if you want because the data for the regression tests are in your phenix installation already):
phenix_regression.wizards.test_command_line_ncs test_find_ncs_from_density cd test_find_ncs_from_density/ phenix.autobuild maps_only=true ncs_file= find_ncs.ncs_spec \ data= cycle_best_1.mtz seq_file= sequence.dat \ ncs_output_mask_file=my_mask_file.map
(The first two commands are just to set up some data that has NCS in it and to find that NCS; in this case 6 NCS copies. You presumably already have done both of these already and so you can go right to the autobuild maps_only step.)
Looking at my_mask_file.map and resolve_work.mtz in the resulting AutoBuild_run_1_/TEMP0/ directory, you can see that one asymmetric unit of the NCS is within region defined by the my_mask_file.map.
I hope that helps! -Tom T
Hi there,
Can phenix generate the NCS masks just like CCP4-NCSMASK does?
Thanks!
Hailiang
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